Beast has been taken away to a maximum security prison and whilst he reads away quietly in his cell, some guards have to laugh at him: a mutant trying to read! Hahaha! The alarms suddenly go off and various bits of the prison start to explode and as the guards shoot they don't seem able to hit whoever the attacker is. Beast is thinking that Wolverine must be trying a rescue attempt but as his cell is ripped apart, someone else floats in.
This person is Magneto, a powerful mutant who is also a master of magnetism. Magneto has come to free Beast and wants him to join up in his plans for conquest. Beast thanks him for his offer but declines, he wishes to stay here as he is due to appear in court. By having a fair trial, Beast hopes to prove his innocence and show that mutants aren't dangerous. Soldiers start shooting at them but Magneto puts up a magnetic forcefield which deflects their shots. Unable to convince Beast on joining with him, Magneto says that mutants are the superior race and that all humans will be crushed. He then levitates out of the cell and sees the soldiers below.
Using his powers, he easily destroys and weapons the troops have, be it rifles, tanks and even helicopters. At the Xavier Institute, Charles and Jubilee watch a report on how the prison was attacked by a mutant.
Xavier explains that he knows who it was: Magneto, or Erik Magnus. Years a go, during a war, Xavier and Magnus were friends who worked at a hospital. Xavier secretly used his mental powers to help heal patients.
However the war continued and one night some terrorists captured one of the patients. Xavier and Magnus went to rescue her, revealing their mutant powers in public for the first time. Whilst they managed to stun the soldiers, Magnus wanted to flat-out destroy them and used his powers to try and crush them to death. Xavier had to stop him and managed to do so, letting the terrorists get away with their lives.
Magnus believed that mutants are a superior race to humans and that humans are flawed in their war-like ways. Calling himself "Magneto", he began to attack factories and government buildings with his growing legion of followers in an attempt to overthrow human society to make way for his mutants to take over. One night, Xavier managed to get to Magneto and used his mental powers on him...
...causing him to fly away in fear. But several years have passed since then and it seems that now, he has returned. The next morning we see a bunch of protestors outside a court declaring how much they hate mutants. Inside the building, Beast's trial has just begun.
Beast explains why he was at the Mutant Control Agency base and that he found out 11 mutants who has recently registered with the M.C.A. have all vanished. The court doesn't believe his claim however and say that he is a threat to everyone, like all mutants, and that the M.C.A. is there to help mutants, not harm them. The judge refuses to grant Beast bail and says that he sees him as a danger to society.
Wolverine is at the trail and wants to show everyone what a danger to society really is but Cyclops stops him. As the two are about to get into a fight again, the arrival of another mutant stops them. Sabretooth has barged his way into the courtroom and begins taking out the guards, demanding that Beast is freed. More guards arrive and begin blasting him. Cyclops wants to save him but Wolverine refuses to help, it seems he knows who this mutant is and doesn't like him.
Cyclops blasts the guards down and rescues Sabretooth. Meanwhile, back at the Institute, Xavier is using Cerebro to try and find Magneto but has no luck. He has to stop however when he finds that Wolverine and Cyclops have returned and have an injured mutant with them.
Cyclops explains that Sabretooth appeared out of nowhere at the trial and that Wolverine apparently hates him, although he doesn't know why. They then see Wolverine in Sabretooth's room, about to kill him! They rush down and prevent Wolverine from doing so just in time. Wolverine says that Sabretooth is a threat and if they aren't going to kill him he'll do it himself.
Xavier says that personal vendettas have no place here and tells Wolverine that if he takes Sabretooth away then he must never return to the institute. Wolverine says they don't know what Sabretooth is like, that he is extremely dangerous being here. Storm then enters and counters his argument by saying that many of them thought Wolverine was dangerous when he first came to the institute. An alarm then goes off: trouble at a missile base! Xavier knows that it must be Magneto and sends Cyclops, Wolverine and Storm to go and deal with him. As Wolverine stomps out he brings up a valid point: why is it they have to go and trash Xavier's enemy, but they have to take it easy on Wolverine's?
At the base, Magneto gets creative with his powers and makes some tanks shoot each other. He then arrives at the launch control building and overrides the computer systems, making every nuclear missile activate! The countdown is started and in three minutes every nuke will launch.
As the X-Men arrived, the launch control staff attempt to over-ride what Magneto has done but fail. The commander of the base then realises that the missiles have been set to land on the base itself! He orders everyone to evacuate immediately, meaning the X-Men get into the base fairly easily.
Magneto finds them and asks if they will join him in his plans for conquest. They refuse and tell him to surrender. Magneto is disappointed that they will not join him and he uses his power to pick them up and then drop them back down, saying that any mutants that don't want to help him are traitors and will be destroyed -and that includes Xavier.
The X-Men get back up and Cyclops blasts down a wall to the launch control building. Wolverine runs in and sets about trashing the place, but with only 5 seconds to go he is too late -the missiles have begun to launch!
Storm starts to fly towards the three missiles and ignores Cyclops' pleas for her not to give up her own life. Cyclops can't shoot the warheads down as if he tried to do it the blast would be to close to them, they'd also die. Storm seems determined to stop them even if she dies in the process but then Xavier contacts her through his mental powers and relays information on the warheads and how they work. She uses her power to create a strong wind which puts the nukes off-course...
...and by using her power of lightning, she fries some of the electronics in each warhead, stopping them from going off as they crash into the sea. Storm is exhausted and drops out of the sky but is saved from going splat thanks to Wolverine. With their mission complete, the X-Men get onto the Blackbird and head back for home.
Nearby, Magneto watches the Blackbird leave and says that Xavier has trained his X-Men well. But he still doesn't understand his old friend's actions, why side and protect with the humans? The very creatures who wish to destroy mutants? Why has he turned against his own kind? To be continued...
NOTES
When we first see Beast, he is reading George Orwell's Animal Farm. Later on at the trial, when he gets sentenced, he says he will "get a chance to catch up on my Dostoyevsky" and is seen holding a copy of Crime and Punishment.
Gambit and Rogue and strangely absent from this episode.